| Metabolite | LogFC | CP | Control | p.value | p.adjust | n_CP | n_Control |
|---|---|---|---|---|---|---|---|
| Phenoxyacetic acid | −1.00 | −2.58 | −1.59 | 1.81 × 10−4 | 9.56 × 10−3 | 40 | 39 |
| 3-aminoisobutyric acid | −0.80 | 0.50 | 1.30 | 3.33 × 10−3 | 4.47 × 10−2 | 40 | 39 |
| Citrulline | −0.38 | −0.83 | −0.45 | 1.53 × 10−3 | 2.95 × 10−2 | 40 | 39 |
| Isoleucine | −0.38 | −0.63 | −0.25 | 3.75 × 10−3 | 4.55 × 10−2 | 40 | 39 |
| Fucose | 0.51 | 3.02 | 2.51 | 3.54 × 10−3 | 4.47 × 10−2 | 40 | 39 |
| Ribose | 0.58 | 1.09 | 0.51 | 3.07 × 10−3 | 4.38 × 10−2 | 40 | 39 |
| Xylulose | 0.73 | 0.95 | 0.21 | 2.73 × 10−4 | 1.12 × 10−2 | 40 | 39 |
| Lactose | 0.78 | 2.09 | 1.31 | 8.41 × 10−4 | 2.13 × 10−2 | 40 | 39 |
| Cellobiose | 0.79 | 1.70 | 0.91 | 2.71 × 10−3 | 4.23 × 10−2 | 40 | 39 |
| Ribonic acid | 0.87 | 1.08 | 0.21 | 1.39 × 10−3 | 2.85 × 10−2 | 40 | 39 |
| Sucrose | 1.24 | 0.85 | −0.39 | 2.97 × 10−3 | 4.38 × 10−2 | 40 | 39 |
| 6-deoxyglucitol | 1.43 | 2.20 | 0.77 | 3.42 × 10−3 | 4.47 × 10−2 | 40 | 39 |
| Mannose | 3.67 | 0.57 | −3.10 | 5.89 × 10−6 | 1.93 × 10−3 | 40 | 39 |
Urine Metabolomics Pancreatitis Differential Results
Purpose
Differential analysis of pancreatitis urine metabolites between Green I and Red patient groups. There is an Executive Summary at the end of this document.
Data
Median normalized metabolite intensities, or metabolite - metabolite ratio data.
Methods
Metabolite abundances in each sample were normalized by calculating the median abundance in each sample, and dividing the abundances by the sample median. Metabolite abundances include only a few zero values (N = 4 across all metabolites and samples) that were subsequently treated as missing. Sample - sample correlations were calculated using information-content-informed Kendall-Tau (ICI-Kt), and median sample correlations used to detect possible outlier samples. No outlier samples were detected, and all samples were used for differential calculations. Prior to calculation of metabolite - metabolite ratios, any missing values were replaced with the lowest observed value for that metabolite across samples. For each normalized metabolite or metabolite - metabolite ratio, a t-test was calculated using the \(log_2\) values in the Red and Green I patients. Any missing values were removed prior to the t-test calculation. P-values were adjusted using the Benjamini-Hochberg procedure (Benjamini and Hochberg 1995).
For association with other patient covariates in the Red and Green I samples, ANOVA was used to perform the statistical test of \(log_2\) values with the covariate, regardless of whether there were only two more more categories. Missing values were removed prior to the ANOVA calculation. Some covariates necessitated special handling prior to ANOVA. Diabetes status (diabetes_bl) required changing all of the “N/A” instances to “Normal”. Etiology status (etiology) required removing all of the “missing” instances (encoded as -999) before the ANOVA.
Results
Direct Comparison
From the direct comparison of metabolites in the Green I and Red patients, 29 metabolites had an adjusted p-value <= 0.05. The volcano plot of log-fold-changes and p-values is shown in Figure 1. The red line corresponds to an adjusted p-value of 0.05.
The table of statistical results is shown in Table 1 and Table 2.
Table 1. Statistics of direct comparisons of named metabolites for patients in control and CP disease groups.
Table 2. Statistics of direct comparisons of un-named metabolites for patients in control and CP disease groups.
| Metabolite | LogFC | CP | Control | p.value | p.adjust | n_CP | n_Control |
|---|---|---|---|---|---|---|---|
| 228072 | −1.25 | −3.61 | −2.36 | 2.36 × 10−5 | 3.87 × 10−3 | 40 | 39 |
| 345452 | −1.21 | −2.79 | −1.58 | 2.04 × 10−4 | 9.56 × 10−3 | 40 | 39 |
| 41866 | −0.94 | −2.45 | −1.51 | 4.10 × 10−3 | 4.72 × 10−2 | 40 | 39 |
| 33983 | −0.75 | −2.27 | −1.52 | 1.11 × 10−3 | 2.42 × 10−2 | 40 | 39 |
| 345144 | −0.61 | −2.61 | −2.00 | 1.69 × 10−3 | 3.07 × 10−2 | 40 | 39 |
| 2091 | −0.50 | 3.96 | 4.46 | 8.42 × 10−4 | 2.13 × 10−2 | 40 | 39 |
| 2082 | −0.49 | 0.20 | 0.69 | 9.23 × 10−5 | 7.57 × 10−3 | 40 | 39 |
| 473743 | −0.47 | 1.35 | 1.82 | 2.30 × 10−3 | 3.77 × 10−2 | 40 | 39 |
| 105379 | 0.58 | −1.00 | −1.58 | 4.18 × 10−3 | 4.72 × 10−2 | 40 | 39 |
| 133590 | 0.60 | 0.71 | 0.12 | 5.98 × 10−4 | 2.13 × 10−2 | 40 | 39 |
| 4901 | 0.70 | 1.17 | 0.47 | 1.07 × 10−3 | 2.42 × 10−2 | 40 | 39 |
| 473342 | 0.75 | −1.35 | −2.10 | 7.65 × 10−4 | 2.13 × 10−2 | 40 | 39 |
| 11353 | 0.76 | 0.80 | 0.04 | 1.20 × 10−4 | 7.85 × 10−3 | 40 | 39 |
| 34113 | 0.79 | 0.87 | 0.08 | 2.11 × 10−3 | 3.65 × 10−2 | 40 | 39 |
| 31764 | 1.35 | 0.64 | −0.72 | 7.94 × 10−4 | 2.13 × 10−2 | 40 | 39 |
| 18242 | 1.68 | −0.07 | −1.75 | 6.65 × 10−5 | 7.27 × 10−3 | 40 | 39 |
Figure 1. Volcano plot of Red - Green I differences. Red line indicates an adjusted p-value of 0.05.
For each of the metabolites with an adjusted p-value <= 0.05, we can plot the distribution of values in the control and chronic pancreatitis (CP) patients to verify the fold-change and p-values.
Figure 2. Raincloud plots of the log2(metabolite) abundances for each group for each named metabolite with a negative log-fold-change. The raincloud plot is a combination of 3 plots: 1 - the original data points; 2 - a boxplot of the distribution; and 3 - a density estimate.
Figure 3. Raincloud plots of the log2(metabolite) abundances for each group for each named metabolite with a positive log-fold-change. The raincloud plot is a combination of 3 plots: 1 - the original data points; 2 - a boxplot of the distribution; and 3 - a density estimate.